From 6727902c3f2d14d55cb0d8b7cfc4826433a7739f Mon Sep 17 00:00:00 2001
From: Ray Speth <speth@mit.edu>
Date: Sat, 15 Nov 2014 00:47:04 +0000
Subject: [PATCH] [Kinetics] Allow skipping third-body efficiencies when using
 Reaction

---
 include/cantera/kinetics/Kinetics.h   | 12 ++++++++++++
 src/kinetics/GasKinetics.cpp          |  9 ++++++++-
 src/kinetics/Kinetics.cpp             |  3 ++-
 test/kinetics/kineticsFromScratch.cpp | 27 +++++++++++++++++++++++++++
 4 files changed, 49 insertions(+), 2 deletions(-)

diff --git a/include/cantera/kinetics/Kinetics.h b/include/cantera/kinetics/Kinetics.h
index 8844a679b..095122e20 100644
--- a/include/cantera/kinetics/Kinetics.h
+++ b/include/cantera/kinetics/Kinetics.h
@@ -814,6 +814,15 @@ public:
         m_skipUndeclaredSpecies = skip;
     }
 
+    //! Determine behavior when adding a new reaction that contains third-body
+    //! efficiencies for species not defined in any of the phases associated
+    //! with this kinetics manager. If set to true, the given third-body
+    //! efficiency will be ignored. If false, (the default) an exception will be
+    //! raised.
+    void skipUndeclaredThirdBodies(bool skip) {
+        m_skipUndeclaredThirdBodies = skip;
+    }
+
     //! @deprecated To be removed after Cantera 2.2. No longer called as part
     //!     of addReaction.
     virtual void installReagents(const ReactionData& r) {
@@ -1084,6 +1093,9 @@ protected:
     //! @see skipUndeclaredSpecies()
     bool m_skipUndeclaredSpecies;
 
+    //! @see skipUndeclaredThirdBodies()
+    bool m_skipUndeclaredThirdBodies;
+
 private:
     std::map<size_t, std::vector<grouplist_t> > m_rgroups;
     std::map<size_t, std::vector<grouplist_t> > m_pgroups;
diff --git a/src/kinetics/GasKinetics.cpp b/src/kinetics/GasKinetics.cpp
index 3145a728e..c78191c63 100644
--- a/src/kinetics/GasKinetics.cpp
+++ b/src/kinetics/GasKinetics.cpp
@@ -375,7 +375,14 @@ void GasKinetics::addThreeBodyReaction(ThirdBodyReaction& r)
     for (Composition::const_iterator iter = r.third_body.efficiencies.begin();
          iter != r.third_body.efficiencies.end();
          ++iter) {
-        efficiencies[kineticsSpeciesIndex(iter->first)] = iter->second;
+        size_t k = kineticsSpeciesIndex(iter->first);
+        if (k != npos) {
+            efficiencies[k] = iter->second;
+        } else if (!m_skipUndeclaredThirdBodies) {
+            throw CanteraError("GasKinetics::addThreeBodyReaction", "Found "
+                "third-body efficiency for undefined species '" + iter->first +
+                "' while adding reaction '" + r.equation() + "'");
+        }
     }
     m_3b_concm.install(nReactions(), efficiencies,
                        r.third_body.default_efficiency);
diff --git a/src/kinetics/Kinetics.cpp b/src/kinetics/Kinetics.cpp
index b8238c420..8ba3d715f 100644
--- a/src/kinetics/Kinetics.cpp
+++ b/src/kinetics/Kinetics.cpp
@@ -23,7 +23,8 @@ Kinetics::Kinetics() :
     m_surfphase(npos),
     m_rxnphase(npos),
     m_mindim(4),
-    m_skipUndeclaredSpecies(false)
+    m_skipUndeclaredSpecies(false),
+    m_skipUndeclaredThirdBodies(false)
 {
 }
 
diff --git a/test/kinetics/kineticsFromScratch.cpp b/test/kinetics/kineticsFromScratch.cpp
index e24252acd..1e3885646 100644
--- a/test/kinetics/kineticsFromScratch.cpp
+++ b/test/kinetics/kineticsFromScratch.cpp
@@ -78,6 +78,33 @@ TEST_F(KineticsFromScratch, add_three_body_reaction)
     check_rates(1);
 }
 
+TEST_F(KineticsFromScratch, undefined_third_body)
+{
+    Composition reac = parseCompString("O:2");
+    Composition prod = parseCompString("O2:1");
+    Arrhenius rate(1.2e11, -1.0, 0.0);
+    ThirdBody tbody;
+    tbody.efficiencies = parseCompString("H2:0.1 CO2:0.83");
+    shared_ptr<ThirdBodyReaction> R(new ThirdBodyReaction(reac, prod, rate, tbody));
+
+    ASSERT_THROW(kin.addReaction(R), CanteraError);
+}
+
+TEST_F(KineticsFromScratch, skip_undefined_third_body)
+{
+    Composition reac = parseCompString("O:2");
+    Composition prod = parseCompString("O2:1");
+    Arrhenius rate(1.2e11, -1.0, 0.0);
+    ThirdBody tbody;
+    tbody.efficiencies = parseCompString("H2:0.1 CO2:0.83");
+    shared_ptr<ThirdBodyReaction> R(new ThirdBodyReaction(reac, prod, rate, tbody));
+
+    kin.skipUndeclaredThirdBodies(true);
+    kin.addReaction(R);
+    ASSERT_EQ((size_t) 1, kin.nReactions());
+}
+
+
 TEST_F(KineticsFromScratch, add_falloff_reaction)
 {
     // reaction 2: